Synopsis

test.RaoBlackwellEstimator [-hV] [--aFi=traj] [--bootstrapIter=100000] [--numSnaps=-1] [--skip=-1] [--sR=<selection>] [--startSnap=-1] [--writeFrequency=100] files…​

Description

Use the Rao-Blackwell estimator to get a free energy difference for residues in a CpHMD system.

Options

--aFi, --arcFile=traj

A file containing the the PDB from which to build the ExtendedSystem. There is currently no default.

--bootstrapIter=100000

Number of bootstrap iterations. Set -1 for no bootstrapping.

-h, --help

Print command help and exit.

--numSnaps=-1

Number of snapshots to use from an archive file. Default is all.

--skip=-1

Calculate energies on snaps with this interval.

--sR, --specifiedResidues=<selection>

Specified residues to do analysis.

--startSnap=-1

Start energy evaluations at a snap other than 2.

-V, --version

Print the Force Field X version and exit.

--writeFrequency=100

Calculate the RBE and print at this snapshot read frequency.

Arguments

files…​

PDB input file in the same directory as the ARC file.